Biochemical interactions

Question 1

What is a receptor?

Answer 1

the site where a drug binds and the receptor brings about a physical response
example - cholinergic receptors and acetylcholine

Question 2

What is a ligand?

Answer 2

ions or molecules that form a complex with the receptor

example - acetylcholine, drug

Question 3

What is the difference between an agonist and an antagonist?

Answer 3

agonist bind to the receptor to produce a biological response

antagonist blocks the action of an agonist. it blocks the active site and binds without a response

Question 4

What are the types of functional groups a protein has?

Answer 4

polar 
non-polar
ionised
neutral 
basic
acidic

Question 5

What are the active sites that a ligand can bind to and what are they made up of?

Answer 5

receptors
enzymes
- both are made up of proteins

Question 6

What are the different interactions that a drug can have with functional groups lining the active site of the receptor or enzyme?

Answer 6

covalent (single) - strongest
ionic 
ion-dipole 
hydrogen
dipole-dipole
hydrophobic 
Van der Waals - weakest

Question 7

What are Van der Waals forces?

Answer 7

weakest type of interaction

• arise because the electron cloud associated with an atom or molecule is constantly moving so the electrons are never evenly distributed = causes unequal charge
• results in small, local, instantaneous dipoles

Question 8

What affects the strength of Van der Waals forces?

Answer 8

the larger the surface area and the larger the number of electrons - the larger the interaction
- surface area dependent

interactions only occur when the molecules are close together

• forces drop quickly if the molecules move far apart
• they are weak and act over a short distance

Question 9

What are dipole-dipole interactions?

Answer 9

permanent dipole-dipole interactions can occur when there is a difference in electronegativities of the atoms sharing chemical bonds
- dipoles will attract one another

bond are stronger than Van der Waals
- it is a electrostatic attraction

Question 10

What is electronegativity?

Answer 10

tendency of an atom to attract a bonding pair of electrons to itself within the atom

Question 11

What are hydrogen bonds?

Answer 11

formed when there are functional groups with N, S or O present and there is an H atom linked to it

• due to the electronegativity difference, the bond is polarised
• the H atom is shared between the donor (O, S or N) and the acceptor (O, S, or N)
• H atom is more strongly bonded to the donor due to the covalent bond

Question 12

When are hydrogen atoms stronger? in a straight line or bent?

Answer 12

hydrogen bonds are directional

- they are stronger when all the atoms/bonds are in a straight line

Question 13

What are ion-dipole bonds?

Answer 13

drugs will ionised functional groups will bind worth permanent dipoles (with an electronegativity difference)
- plays a role in water solubility of a drug

Question 14

What is ionic bonding?

Answer 14

formed between species with opposite charges

- can act over long distances and are strong

Question 15

What is covalent bonding?

Answer 15

majority of bonds within drugs and their targets are covalent
- are strong = drugs forming covalent bonds are usually permanently bonded to their target

Question 16

What is an example of covalent bonding in drugs?

Answer 16

anti-cancer drugs, mechlorethamine, can alkylate DNA in tumour cells. It links the strands together.
- makes them unable to function so the cell dies

alkylation - addition of an alkyl group

Question 17

What is the difference between water molecules in liquid water and in ice?

Answer 17

a system will adopt the lowest energy configuration - meaning it will attempt to make as many bonds as possible

liquid water molecules - H bonds are continuously forming and breaking

ice water molecules - forms 4 H bonds
- O can make 2 bonds and H can make 1 each

Question 18

How does water solvate (dissolve) other molecules?

Answer 18

a shell of water forms around polar molecules

- stops them from interacting with one another

Question 19

What is hydrophobic attraction?

Answer 19

water cannot bond to oil so it forms a cage around oil droplets by having H bonds with each other
- increases the energy of the system = fewer H bonds and entropy decreases

if there are two droplets
- two droplets result in the system having high energy = entropy decreased for both

make one large droplet

• releases some molecules back into the solution
• increases entropy of the solution as there are more molecules

Question 20

Why is optical, geometrical and conformation isomerism important for drug binding?

Answer 20

optical
- drugs must be administered as single enantiomer as mirror image can have adverse effects
geometric
- rotation around a double bond
- cis = molecules on the same side, trans = molecules on opposite sides
conformational
- molecules can adopt preferred shapes
- drug binds more easily if its preferred conformation fits the active site

Question 21

List the types of interactions a drug can have with an active site.
List them from the strongest to the weakest interaction.

Answer 21

covalent, ionic, ion-dipole, hydrogen bonding, dipole-dipole, hydrophobic and Van der Waals

Question 22

What are the two key requirements necessary for hydrogen bonding to take place?

Answer 22

Hydrogen directly bonded to an electronegative atoms such as O, S or N, thus generating a polar bond.

An hydrogen bond acceptor, something with a lone pair or slightly negative end